rootDir = ..
include ${rootDir}/include.mk
modObjDir = ${objDir}/synteny

halSynteny_srcs = impl/halSynteny.cpp impl/hal2psl.cpp impl/psl_io.cpp impl/psl_merger.cpp
halSynteny_objs = ${halSynteny_srcs:%.cpp=${modObjDir}/%.o}
srcs = ${halSynteny_srcs}
objs = ${srcs:%.cpp=${modObjDir}/%.o}
depends = ${srcs:%.cpp=%.depend}
inclSpec += -I${rootDir}/liftover/inc
otherLibs += ${libHalLiftover}
progs = ${binDir}/halSynteny

all: progs
libs:
progs: ${progs}

clean : 
	rm -rf ${objs} ${progs} ${depends} output

test: test1

test1: output/rand1.hal
	../bin/halSynteny --queryGenome "Genome_14" --targetGenome "Genome_18" $<  output/$@.psl
	diff tests/expected/$@.psl output/$@.psl

output/rand1.hal:
	@mkdir -p output
	../bin/halRandGen --seed 0 --testRand --format hdf5 $@


include ${rootDir}/rules.mk

# don't fail on missing dependencies, they are first time the .o is generates
-include ${depends}


# Local Variables:
# mode: makefile-gmake
# End:
